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- PDB-6hjz: Xray structure of GLIC in complex with succinate -

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Basic information

Entry
Database: PDB / ID: 6hjz
TitleXray structure of GLIC in complex with succinate
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / Pentameric Ligand-Gated Ion channel
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / transmembrane transporter complex / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DIUNDECYL PHOSPHATIDYL CHOLINE / SUCCINIC ACID / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsFourati, Z. / Delarue, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency13-BSV8-0020 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel.
Authors: Fourati, Z. / Sauguet, L. / Delarue, M.
History
DepositionSep 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
D: Proton-gated ion channel
E: Proton-gated ion channel
F: Proton-gated ion channel
G: Proton-gated ion channel
H: Proton-gated ion channel
I: Proton-gated ion channel
J: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,72498
Polymers362,77710
Non-polymers27,94688
Water3,837213
1
A: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
D: Proton-gated ion channel
E: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,36249
Polymers181,3895
Non-polymers13,97344
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39440 Å2
ΔGint-218 kcal/mol
Surface area61560 Å2
MethodPISA
2
F: Proton-gated ion channel
G: Proton-gated ion channel
H: Proton-gated ion channel
I: Proton-gated ion channel
J: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,36249
Polymers181,3895
Non-polymers13,97344
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39470 Å2
ΔGint-220 kcal/mol
Surface area61250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.713, 132.489, 320.565
Angle α, β, γ (deg.)90.00, 102.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 22 molecules ABCDEFGHIJ

#1: Protein
Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC


Mass: 36277.723 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria)
Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#5: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 289 molecules

#2: Chemical...
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C4H6O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM NaSuccinate pH4 400 mM NaIsothiocynate 12-15% PEG4000 2% DMSO 15% glycerol

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.5→12 Å / Num. obs: 254093 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 68.46 Å2 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.7 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 2.5→12 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9276 / SU R Cruickshank DPI: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.214 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 12655 5.03 %RANDOM
Rwork0.2168 ---
obs0.2173 251740 99.7 %-
Displacement parametersBiso mean: 75.49 Å2
Baniso -1Baniso -2Baniso -3
1--4.722 Å20 Å217.3835 Å2
2---0.282 Å20 Å2
3---5.004 Å2
Refine analyzeLuzzati coordinate error obs: 0.433 Å
Refinement stepCycle: 1 / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25258 0 1030 213 26501
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00826871HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0536454HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9272SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes521HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3812HARMONIC5
X-RAY DIFFRACTIONt_it26871HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion18.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3531SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact29968SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 906 4.85 %
Rwork0.2622 17784 -
all0.2617 18690 -
obs--99.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5975-0.32970.32550.388-0.23431.1640.09750.04150.15070.04370.0089-0.0139-0.2209-0.1878-0.10650.13080.0886-0.1757-0.05640.0587-0.1883-50.387219.598330.2815
21.08490.01290.92420.24820.22541.52920.03540.0199-0.04860.1088-0.03390.1295-0.0244-0.1241-0.00150.02260.011-0.19690.0408-0.0091-0.151-62.3032-1.70636.4544
30.71620.14260.89030.56040.27862.06290.01410.0504-0.19020.0409-0.04360.05790.105-0.02350.02940.06230.0158-0.2472-0.0762-0.061-0.1084-48.1113-21.174329.7338
40.6143-0.00050.55590.34760.29172.04980.00880.1197-0.1686-0.0581-0.024-0.1202-0.01520.10050.01520.05280.0497-0.2095-0.0495-0.0928-0.1267-27.221-12.079618.8387
50.641-0.16930.680.3859-0.4612.28160.08160.07990.1409-0.0546-0.0466-0.1673-0.15380.0233-0.0350.13150.028-0.1755-0.09150.0314-0.1557-28.707213.256519.2866
60.60180.07860.62640.6360.1641.246-0.00620.07990.0846-0.03390.0842-0.0784-0.10330.079-0.0780.103-0.0291-0.14-0.1201-0.0024-0.100815.956821.4074125.9732
71.4949-0.83992.05611.3454-1.13293.31480.15330.1145-0.20390.12590.1123-0.20020.19910.0736-0.2656-0.2758-0.09680.11360.0520.0368-0.147228.19710.315120.1602
80.4858-0.0260.26960.486-0.08160.98450.0337-0.0036-0.2231-0.0316-0.0285-0.03370.126-0.0189-0.00530.0799-0.0196-0.1938-0.14850.0299-0.044214.1036-19.1285127.4286
90.583900.58090.517-0.35522.07640.00490.0181-0.09710.12660.00410.1396-0.05-0.0956-0.00890.07-0.0332-0.1659-0.16230.0331-0.0603-6.8131-10.2489138.3373
100.63370.10170.56840.51920.33271.42530.01540.04990.13260.0924-0.04250.1389-0.0933-0.03570.0270.09730.0245-0.138-0.1598-0.0087-0.0601-5.759214.8525137.169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }

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